Hidden Pain
by Fyrewire
Summary: After a mission that nearly costs him his life Rodney begins acting strange... Can Sam save him or will she lose him to the darkness?
1. Chapter 1

From the brain that brought you 'McKarter drabbles' And 'Beware the plot twister' I give you… My first angst! YAY! And tragedy… Not yay.

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Sam sighed as they walked through the ruins. She didn't see the point in her coming on this mission but if she spent one more minute on Atlantis she would go insane.

It was an uninhabited planet that had what was believed to be an ancient lab.

"Colonel Carter." Came McKay's voice.

"Yes?" she asked.

"Come check this out." McKay said.

"Coming." She sighed.

Waking over to the lab McKay was investigating (For lack of a better word) she wondered what kind of pointless thing McKay had found.

Entering the lab she saw McKay standing over a panel trying to turn it on.

"What are you doing?" She asked.

"I've figured out what this lab was used for… It was to create some sort of super soldier among those with the ancient gene." He said distractedly.

"McKay…" Sam said with a worried look on her face. "You're not going to do anything stupid… Are you?"

"Oh please… Since when have I ever done anything stupid?" He asked.

Seeing Sam giving him 'the look' he muttered, "That doesn't count."

Sam rolled her eyes and stood against the wall as McKay tried to activate the machine.

"Are you trying to turn yourself super human again?" She asked.

"No!" McKay said quickly. "It's just that. His lab uses a lot, and I mean a _lot_ of power. So there's a good chance the ancients working on it had a storage of ZedPMs somewhere!"

Sam's head shot up and realization dawned on her face.

She was about to say something when the machine McKay was working on whirred to life.

McKay grinned. "Now we're getting somewhere." He said.

He hit some buttons to activate the database when his hand slid over what looked like an activation pad.

An electric shock came out of the machine and ran through his body before he collapsed.

Sam ran over to him.

Placing her hand on his neck she desperately searched for a pulse. Nothing.

She quickly pressed the button on her radio.

"Radio Atlantis. McKay isn't breathing."

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I feel that at this point I should clarify that this is NOT A ONE SHOT

Dedicated to all who have waited for it.


	2. Chapter 2

Notes to reviewers of last chapter:

Leliana McKay: Thanks. It took me a while to write it. I hope you like the rest of the story as well.

Sam Carter McKay: Glad you like it. Hm… Are you sure that's a smart idea?

Janib: Thank you for reminding me of that. I forgot to put in mentions of CPR.

Miss. Pookamonga: If you think that will help my stories a bit then I'll try to remember to do that. Thank you for the praise. You are one of my most dedicated readers… (Pauses and looks at other readers whom are carrying pitchforks and torches.) Not that you aren't… Now, now… No need to go 'Frankenstein angry mob' on me… I write this story! (Screams)

Unknownterra: (tied to a stake with villagers preparing to burn) Thank you. I'm glad you like it.

Samandjackforever: I'm going to assume that means you like it… Hey. Is it just me or is it kind of hot? (Looks down) Oh. Right. They lit the fire… Goodbye everybody.

And remember… Reviews are love!

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Later when they got back to Atlantis, Sam was watching over Rodney while he was unconscious in the infirmary.

It had taken two minutes of CPR to revive him… Two minutes where he was dead… Two minutes where Sam thought she would lose him…

Dr. Keller had finally stopped bothering her with questions about what happened and left her to watch over Rodney.

She sighed. Part of her was saying it was his own stupidity but the larger part was saying it was her fault for not stopping him and convincing him to check it out later with a team.

She sighed. She was supposed to be their leader and she could barely keep the head scientist from killing himself.

Sometimes she wondered if he did things like this on purpose. Dangerous things that if done wrong, or right, could be suicide.

Of course there were times when she herself had done things like that in hopes of ending it all.

The job… And the stress really got to her sometimes. Sometimes it was too much.

Glancing at McKay she hoped he hadn't gained the suicidal tendencies she had finally managed to leave behind.

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Whoa… Sam was suicidal? Whoa…

If you want to save me I need at least ten reviews.


	3. Chapter 3

Notes to reviewers of last chapter:

Llanea: Thank you. I'm glad you like it so much

Leliana McKay: In some stories it's hard for me to make long chapters and still have it give out the point I'm trying to make… Suspense… I feel that Sam may be a tad suicidal in the show… Why else would she try so many dangerous things? Anyway. Sam being suicidal fits in with the ending I have planned.

Samandjackforever: Thx for liking it so much.

Sam Carter McKay: Thank you for pointing that out. I've gone back and fixed it.

Lala: Evil. Little. Anonymous. Reviewer.

Janib: Meh. See Leliana McKay's response.

Miss. Pookamonga: I think we share a brain…

And here's the long awaited third chapter.

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"Rodney's awake" Was the first thing colonel Sheppard said upon entering her office.

She jumped up from her chair at these words.

"Let's go." She said.

She was already out the door so she didn't see John smile at her knowingly.

When Sam reached the infirmary she was surprised she didn't hear Rodney snarking to be let out.

Peaking in she saw that he was, in fact, awake.

"I'm surprised you haven't driven the medical staff to insanity yet." She said while stepping into the room.

A spark of worry formed in the back of her mind when Rodney only shrugged and mumbled incoherently.

"Are you all right?" She asked.

"Yes." Rodney said hoarsely.

She still was worried. Something seemed off about Rodney. She just wished she knew what.

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Heating u-u-up… Anyway. I need five new, note the new Lala, reviews for the next chapter… And if anyone wants to they can send me suggestions on how to make the chapters longer. 'Cause after I finish posting this version I was hoping to post a longer version.


	4. Chapter 4

Notes to reviewers of last chapter:

Bex: I think we'd all like to see a little more McKay. You know you set me up for that.

Sam Carter McKay: Thanks for the tip. After I complete this version I'll start on the longer version.

ZedPM: Thank you.

Miss. Pookamonga: (Smirks) That was the kind of reaction I'm looking for in my reviewers when I wrote this chapter.

MBB: Yes I believe the ratio has shifted that way.

M: Thank you or the complement. Don't touch my moustache (Laughs to self at Toy Story 2 reference)

SciFOXCraft279: You are a nice person. I hope you find a hundred dollar bill in your sock drawer. (Looks at the jealous reviewers) Whaaaaaattt? She gave me the most complements this chapter.

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It had been a week since Rodney woke up. He had been cleared for lab duty but still was not allowed to go off world.

Sam was having some scientists keep an eye on him because he still seemed different… Even if she was the only one who noticed.

"Col. Carter." She heard Dr. Zelenka say.

"Yes?"

"You're right. Rodney has been acting strange ever since he woke up… I'm… Worried about my friend."

"I'm worried about him too." She said with a sigh.

Radek looked at what she was reading.

"What is that?" He asked.

"I managed to find some information on the lab in the database. I haven't found much stuff of interest yet." Sam sighed.

"Well. Let me know if you do." He said before leaving.

Sam nodded and went back to shifting through the database for something, anything, that would tell her what was wrong with Rodney.

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G2G: We're having tacos tonight


	5. Chapter 5

Notes To Reviewers Of Last Chapter:

Sam Carter McKay: I'm glad you think that.

Llanea: I hope you're still alive. And my tacos were delicious.

Janib: Well of course! McKay just isn't McKay unless he's the snarky scientist we all love (Glomps Prisoner!McKay)

Miss. Pookamonga: Writer's block doll. This chapter was so short because of writer's block.

Casperace13: (Even though you reviewed chapter 1 I'm posting your review here) Because I can! And I love the pairing.

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It was around midnight when Sam decided that she couldn't sleep anymore.

She sighed as she walked through the halls of Atlantis. She just didn't get it.

It had been a month since Rodney had woken up and so far only she and Radek had noticed that something was wrong.

On top of that, at times Rodney seemed like the old McKay.

It just didn't make sense…

Somehow she found herself in McKay's lab.

He was still there. Working like there was no tomorrow.

It was times like this when she wondered if she and Radek were just imagining the way Rodney acted.

But then something would happen and Sam knew that something was seriously wrong with Rodney.

"Anything you want?" He asked without even looking up.

Like that. He never noticed her in the lab if he was wrapped in his work.

"No. Just wandering around and ended up here." She said.

"Well be quiet… I have work to do." McKay snapped.

"I didn't say anything until you asked me why I was here." Sam snapped.

"Are you still speaking?" He asked.

"Actually I'm leaving now." Sam growled before storming out of the lab.

Rodney looked up and watched her go. A smirk was tugging at his lips.

After he was sure that he was alone he whispered, "You and Zelenka are the only ones who notice something wrong with your Dr. McKay… Even if you do lead the expedition and Zelenka is a respected scientist… You will never be able to convince everyone that something is wrong with him time. In a matter of days I will have full control of this body and Dr. Meredith Rodney McKay will be a fleeting shadow trapped within his own mind…"

A cruel chuckle escaped his lips and somewhere deep within his mind the real Rodney McKay screamed in pain as the monster that had taken control of his body slowly killed him.

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Sorry it took so long with this. And I'm probably not going to get the next chapter up till after new years day. 


	6. Chapter 6

Notes to reviewers of next (Oops I mean last.) chapter

Llanea: Thank you.

Leliana McKay: Thanks. And ri-i-i-ight… Now because we all know everyone just reads the replies to their reviews.

Miss. Pookamonga: BOO!

Stargate fan: Thank you for your praise. Ma-a-a-a-y-y-y-y-be.

And I noticed that this seems to focus on Sam a lot so I'm adding a chapter showing what happened to McKay since he touched the panel.

1st person.

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I remember what happened after I touched the panel quite clearly.

There was a shock and then a feeling of detachment. As if I'm no longer connected to my body.

I remained just lying where I was with my eyes closed for a few minutes. Wondering whether or not I had died, and cursing my stupidity if I had.

I remember a dark voice sounding throughout the area. Even now the words he said sends chills up my spine.

"Welcome to your new home Dr. McKay…"

The taunting way he said my name was enough to get me to open my eyes.

I was shocked at what I saw.

There was nothing but blackness around me. I was surprised I could see anything.

I couldn't see the source of the voice. I suppose now it's only logical that he was behind me.

"Where am I?" I had asked him.

A laugh sounded throughout the area before the voice said, "In the deepest recesses of your mind. Where you can't interfere with my plans."

"What? What plans? Show yourself!" I shouted.

"As you wish." (AN: Sorry to any Princess Bride Fans who were greatly disturbed by that)

I felt myself being turned by force unknown. And when I saw the thing I was shocked beyond words.

It looked like… Me.

After a moment or two I regained my ability to speak and started screaming questions.

After a while he grew annoyed and waved his hand. Apparently making so I couldn't speak.

"Now. I know you have some questions so I will answer a few as I see fit. Your body is currently in a coma in the infirmary of Atlantis. It will awaken in three weeks. But you will no longer be in control. I will." A smile that sent pangs of terror down my spine formed at his lips.

"No one will notice that you aren't yourself until it is too late. I will be able to take control of Atlantis and, eventually, Earth. Yes. I know about your precious planet. I have gone through your memories and know everything about you. It will be wonderful to witness the look in your sister's eyes when her dear brother murders her family and her."

I'm full of energy at those words. I dive at him intent on wrapping my hands around his neck and strangling him.

He looks bored, as if he had expected this.

He waves his hand again and sends me back into something. Maybe he generated something for me to hurt myself on, to show me how much control he has even in my mind.

"Do not try that again. I can cause you pain even in your mind." (AN: Mental pain! Sorry) The man hissed before disappearing.

So now here I am.

I'm resting in the darkest corners of my mind. I feel as if I have just been fed on by a wraith.

I can't believe what that bastard is doing, and has done, to me.

He's taken over my body.

Now he wants to take over my soul.

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Finally, eh? And aren't you ecstatic that SGA won best Sci-fi in PCA?


	7. Chapter 7

Notes to reviewers of last chapter (Wow! Only two this time):

Miss. Pookamonga: Yes. Thank you. Hope you like this chapter

CowGrl: Thank you. I like to be unpredictable.

Now back to Sam.

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Sam sat at her desk searching the file on the outpost they had found. The one McKay had been electrocuted at.

She had barely scratched the surface. Because every time she sat down to read it someone interrupted her.

Not now. She had gone to the south pier and turned off her radio. It was necessary in order to find out why the outpost was shut down. Why Rodney was acting so strange. If Rodney was in danger.

Sam shook her head to clear her thoughts. She needed to focus.

After hours of searching (She was fairly certain that the staff was in a panic by now) she found something.

Status report filed by: Hellioneta

Everything was going so well. We thought that we'd made real progress with this.

But then we found the unseen side effect…

While the subject gains superior strength speed and thinking ability we have discovered that it costs the subject something great.

Their free will.

With what we thought was major success we have recently discovered to be a terrible failure.

When the subjects come in contact with the machine their own will is suppressed and a new one takes control.

And the new consciousnesses are completely evil…

We have found a way to destroy the new consciousnesses and save the old but the old are never the same. Inside their mind the new consciousness tortures them while destroying their entity. Many subjects have been found to be alive but unresponsive after the new consciousness is destroyed. The others often beg for death.

We advise that the facility be shut down and no one step foot on the planet again.

End status report.

Sam stared in shock at her computer. Could that really have been true? If so. Was it happening to Rodney?

Sam slammed her computer shut and stood up. She needed to present her findings to Radek so they could discuss options.

She turned and ran into the hallway.

After a minute of running something hit the back of her head.

Sam fell to the ground. Groaning when she felt something warm dripping down her neck.

Sam turned around. There, standing in anger, was Rodney.

"You shouldn't have gone pocking your nose in things that aren't your business. Colonel." The last part was said with so much disdain. So much hatred. That Sam knew what had been described in the report had happened to Rodney.

"Funny." The thing controlling Rodney said. "While you thought he was just toying around and flirting with you… He was actually in love with you. Not that I care. But I suppose that with you in a coma in the infirmary you won't really care either." He absently rubbed his shirt.

"Why." Sam coughed. Blood sprouting around her lips. "Why just put me in a coma? Why not kill me?" She asked.

He sighed.

"Because it would seem suspicious for the expedition leader to suddenly die. I need to make it look like I came looking for you and found that something in one of the un-searched labs exploded and I found you barely alive." He pointed to a gaping hole in the wall and shrapnel embedded in another side.

"It would seem that you were in the wrong place at the wrong time, Colonel." He laughed slightly while Sam's vision slowly faded to black.

As soon as Rodney's controller was sure that Sam was passed out he pressed the radio and changed his voice to one of worry.

"Med team to hallway B5 by the north pier! Something in one of the labs exploded and a piece of wall hit Sam in the back of the neck. She's having trouble breathing!" He turned the radio off and smirked at the colonel's unconscious body.

Now he just needed to take care of the annoying Czech and no one would stand in his way.

It would seem far less likely to be murder if he were killed fixing an overloading generator…

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OH-NOES! Evil!McKay is going after Radek! And what will happen to Sam? Stay tuned faithful readers.


	8. Chapter 8

Notes to reviewers of last chapter:

Miss Pookamonga: As my writing evolves my story grows greater. Let me tell you, it is nearly impossible to write angst after seeing kung fu panda, but I try my best and hope for it to work out.

Cowgrl: Neither do I, but my story centers on the idea of McKay being evil.

Leliana McKay: Thanks. And You may not be too happy with what I do to Radek and Sam.

On with the show! Which I still don't own.

--

Dr. Jennifer Keller watched as air was pumped into Sam's body. She had gone into repertory arrest just as they got her to the infirmary. The blow she'd taken had been more damaging than they'd originally believed.

It was lucky that Dr. McKay had been going to ask her something when it happened. Or else… Who knows what would have happened.

Footsteps coming up behind her brought her attention away from Sam. Dr. Zelenka was standing next to her.

"Hey." She whispered. Glancing at him.

"I just heard." He murmured, barely audible.

Jennifer sighed.

"Ever since she got here her vitals have been all over the place. Sometimes it's like she's about to die, other times it's like she might start breathing on her own." She sighed.

"It's like something's keeping her from waking up."

Zelenka looked at the frail body of their commander, it was nearly impossible to believe that she was like this, she always seemed so strong, never giving in.

And yet, something as simple as a malfunction in a lab had brought her to the brink of death…

Late that night a lone figure slowly snuck into the room where they kept the west naqauda generator and took out a small device, it was simple in appearance but could cause more harm than the Earth weapons the teams on Atlantis used.

It could create a wild yet controlled explosion, ranging from just enough to destroy one object to enough to incinerate a body.

He had created it himself, after taking his host, with the man's already incredible brainpower combined with the enhancing effects of the machine that had implanted him, meant that he was one of the smartest of his kind.

Casting a quick glance around he knelt down and set the device in a crevice on the generator and pressed a button on it, causing a light to blink on for a moment before becoming invisible.

Hearing a clang behind him he turned around to see that annoying Zelenka man standing next to a tipped over table, nothing important, just a table with screwdrivers and such on, but enough to be a disturbance.

"Rodney? What are you doing here?"

"Oh, uh…" His mind raced for an explanation, he found himself shocked that he didn't have one prepared.

"I was coming down to check on the generator, the computer was showing some weird fluctuations, must have just been a glitch in the screen because everything's fine."

Mentally congratulating himself for coming up with that explanation in two seconds, he watched as Zelenka, obviously not buying the explanation, walked over to the generator, looking it over.

When he found nothing wrong he cast a look at him before saying:

"Are you hungry?"

"Yes, extremely so." He remembered from his host's memories that he ate more often than the average human.

"The cafeteria is still serving."

"Excellent."

They walked off, and Radek couldn't help but feel a sense of normalcy, even with colonel Carter in critical condition and Rodney acting stranger and stranger every day, he felt like, maybe he and colonel Carter were wrong about something being wrong with Rodney, and it was all in their heads.

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Sorry for the long time to update, my explanation is on my account page. Hope you liked.

Oh BTW: I have this weird fan fiction idea going around in my head where Dr. Kavanagh is really a woman crossdressing as her brother, the real Dr. Kavanagh.

PS: If anyone knows the rules for posting fanfiction challenges, please tell me.


	9. Chapter 9

Notes to reviewers of last chapter:

Samandjackforever: Aheheheh… Not quite ASAP, but it's an update.

Miss Pookamonga: Um… You may not like the end of this chapter any better. (Smiles.) Oh yeah. KFP was great. WallE was good too.

(My ratings:

KFP: 7.5/10

WallE: 9/10)

Hunterofshadow: Yes. It has been a while, huh? And that was the intention.

OMG! I am so sorry it took so long to update, please don't kill me! A comic book I'm writing is taking up all my time.

--

Jennifer watched as Rodney sat next to Col. Carter. He wasn't saying anything that she could hear and he wasn't taking his eyes off of the datapadd. Even with the way he looked completely disinterested in the comatose woman lying next to him she knew that he must be really worried over her.

Rodney's padd beeped and he looked at it for a minute before pressing his comm.

"Radek. Generator three is showing those weird fluctuations again. Go check on it." He went back to looking over padd while Jennifer amusedly listened to the grumblings of the irate scientist through her own comm. Link, she had tapped it into Rodney's using the little tech knowledge she had, not really having anything better to do and finding listening in on the scientist's chats amusing. She thought it was sweet that Rodney didn't want to leave Col. Carter's side.

She smiled and quietly slipped into her office, she didn't want to disturb him.

After about a minute the grumblings faded to the sound of him making the noises of a scientist deep in thought.

"There's nothing wrong with the machine, Rodney." Radek's voice came over the comm.

"Keep checking. These fluctuations have been getting wilder lately. I want to make sure that _absolutely_ nothing is wrong." Rodney said, tapping a few more things on his padd.

Radek went back to grumbling for a few seconds before a high-pitched whining filled the comm. Link, causing Jennifer to flinch and she would have taken the link out of her ear had it not been for the dark chuckle that was heard across the comm.

"Rodney?" Radek's voice was small, scared. He sounded more like a child separated from his mother than anything else then. "Rodney the generator is overloading.

Rodney's cruel smirk was evident in the voice as his voice filled the ears of both Jennifer and Radek.

"I know."

It was in that moment that Jennifer was no longer seeing the caring yet cold Rodney McKay. But a sadistic killer.

"Don't bother trying to escape. I've locked the doors. You should have kept your nose out of my business, Radek. Col. Carter made the same mistake."

Jennifer had to cover her mouth to keep a gasp from escaping; from the way he spoke she just knew that it would be bad if her knew she was hearing this.

"Rodney. What-"

"Rodney is as good as dead. I took control of his body in the weeks he was in a coma."

Jennifer bit down into her hand hard enough that her mouth filled with the acrid taste of blood.

"With you out of the way there will be nothing holding me back. Goodbye."

Rodney pressed the final bit of code on his datapadd and an explosion rocked Atlantis.

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Finally! It took me forever to come up with an idea for this chapter…

(Pause)

Man this'll be hard to follow up. Anyway. I've got how Sam'll wake up all planned out.


	10. Chapter 10

Notes to reviewers of previous chapter (Wow, only two, did I do something wrong?):

Miss. Pookamonga: Thank you for your sheer detirmination for my continuation of this story (Don't worry, plan on seeing this through to the end), and if you read my profile you'll know that the reason I didn't update until now was because of NaNoWriMo…

Samandjackforever: Thank you for liking it so much, and sorry I couldn't be as prompt as you wished.

This chapter might get a bit confusing, it mostly contains Jennifer's inner debates.

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Jennifer walked silently through the halls of Atlantis two days later, barely registering where she was going as she tried to comprehend what she had learned just before Radek's death.

She inhaled sharply as the thought crossed her mind, he had been killed almost instantly by the blast, dead by the time she got to him.

He had been burned horrifically by the radiation, it would have been beyond recognition had it not been for the DNA tests they'd done.

Jennifer had known who it was before the DNA tests came back, how could she not, after what she heard?

When it had been confirmed that it was Radek she had seen Rodney's eyes show sadness, but she had seen that it was forced.

The science team had held a candlelight vigil for Radek that night, honoring their passed friend and co-worker, despite the science staff holding it many had shown up from the military, kitchen staff, medical staff (her included)

When she was there Jennifer couldn't help but notice that Rodney had been absent, when she asked a scientist about she'd said that the head of department had left for his quarters with a depressed look on his face.

Jennifer let out an angry sigh as she remembered how sincerely the scientist had believed that Rodney was truly mourning a friend too much to be around people as she opened the door to her quarters, which she had somehow managed to end up in front of, and walked in (Closing the door behind her) before collapsing on the bed.

Rodney… Wasn't Rodney. Whatever he was now, it was pure evil, definitely not the kind hearted, but rough on the outside, hypochondriac she'd come to consider a friend.

She let out a sigh, what was she supposed to do with this knowledge? There was no way she could take Rodney, it, not Rodney, it, down on her own, and what were the odds of anyone believing her?

She clenched her hand into a fist and pounded on the mattress, glaring at the ceiling and biting her lip, letting out a frustrated groan.

She should do something.

What was she supposed to do?

She could lure him out.

Like that would work, even if it wasn't Rodney he was obviously still way smarter than her.

She could get help.

As she had stated before, 'who would believe her'?

She could stop him.

How? It was only pure luck that it hadn't found out that she knew already.

Jennifer rolled over and stared blankly at the wall, thinking nothing yet at the same time her mind was running a million miles a minute.

She could monitor him, the second he started to act suspicious she would corner him.

Jennifer snorted at the thought, and the CTV feed had just coincidentally stopped for a few minutes in the labs each night… She'd been bored three nights ago, give her a break.

She could… Oh, what was the point? There was no possible chance of getting the upper hand against him.

She sighed and rolled over, closing her eyes before they snapped back open.

How could she not think of that? Well, it was an ancient experiment that the results of which had never been posted, but what choice did she have?

She sat up quickly and pulled out her data padd before shaking her head and forgoing it in favor of good old fashioned pen and paper, she didn't need Rodney, not Rodney, hacking in for some reason beyond her understanding.

Jennifer brought back the data padd, mentally smacking herself for forgetting to check the experiment's records before she started to write anything down, and started sifting through the ancient medical records.

Maybe, if everything was done correctly, it would work. Maybe she could…

--

Cliff hangers: writer's crack.

Plain and simple.

I'll try to get the next chapter up as soon as possible, but I want to let ya'll stew in this for a while.

Please let me know if you think that this chapter was lacking, I really like advice.

Oh, BTW on my NaNoWriMo… Made it (High fives and dirt cake all around)

Oh man, now I'm craving dirt cake.

Google that, it's not what most of you are thinking.


	11. Chapter 11

Notes to reviewers of last chapter:

Angw: Stop guessing plot points! But, seriously, good guess.

Miss. Pookamonga: Happy holidays! And you stop guessing plot points too!

This chapter will be kind of short, but I'll make sure the next one's longer.

--

He walked through the hallways, he was going to do it, today, he just had one thing left to do.

He almost didn't notice the feeds being accessed… Almost.

In truth he almost cast it aside, figuring that it wasn't worth his time, but then he decided not to make the same arrogant mistake his host would have.

He traced who was monitoring the CCTV feed back to her, she knew what was going on, he just knew it.

Well, he could not have her getting in his way, he'll just have to… Dispose of her.

He reached the infirmary and looked in, she was taking readings on Col. Carter, no one else was around… Perfect.

His eyes narrowed and his muscles tensed before he launched himself across the ten feet, landing right behind her.

She turned around quickly, her eyes widening in shock. "Rodney, wha…?" He cut her off with a quick strike across her abdomen, knocking her back into some of the machines hooked up into Col. Carter.

He gave her no time to retaliate, no time to scream, he gave a sharp uppercut to her jaw and kicked her knee hard enough for a resounding 'crack' to echo in the empty infirmary.

He continued to attack her until he was satisfied, her laying on the floor bleeding and moaning in pain.

He turned around and walked calmly out, glancing at a mirror by chance on the way.

He smirked at what he saw looking back at him, he saw Rodney, same old Rodney, only he now had deep, blood red eyes.

What he didn't see was Dr. Keller slowly pull herself up and grab a syringe, her breath was labored and she was close to dying, but she had one last thing to do.

The second he was out of the infirmary she jammed the syringe into Col. Carter's neck and pushed down on the plunger before falling to the floor with one last thought.

_Please let this work…_

--

Confusing? Good? Bad?

I should wrap this story up in the next five chapters but I'm not sure.

Happy holidays everyone, and check out my other story "Dr… I'm sorry, what was your name again?" (Shamelessly self-promotes.)

PS: I'm sorry if there aren't any things separating the chapter from the notes, but I swear I put them in, they just never show up for some reason.


	12. Chapter 12

Notes to reviewers of last chapter:

Teachergal: I _do_ put the separators in, but sometimes they won't show up. Glad you like the story.

Samandjackforever: Okay! Updated quicker than I expected.

Miss. Pookamonga: Yes... Nearly.

--

John sat behind Sam's desk in the control tower, filing through recent reports, he himself had been so busy since Colonel Carter's accident that he hadn't had much time for anything, he honestly didn't understand how the woman managed to do it.

"Sir." Lorne appeared in the door.

"Major." He nodded.

"Dr. McKay's here to see you, says it's important."

John sighed, Rodney tended to think that most of his discoveries were, quote: 'Important'.

But he hadn't heard of one of Rodney's discoveries for quite some time, which in itself was strange, maybe he'd been working on a big project and wanted to get it perfect before showing him.

John nodded.

"Send him in," Lorne moved to leave when John added, "but tell him that if this isn't the best damn thing he could get me he's outta here." Lorne chuckled, after all, with everything that's been going on they needed some way to keep their spirits up.

About a minute after Lorne left Rodney walked in and closed the door before pressing a few buttons on his datapadd to make the windows facing the control tower go black, leaving whatever light they could get coming in through the outer facing windows.

"Okay Rodney. What's this 'important thing' you wanted to tell me?" John asked as Rodney walked over to look out the window.

"It's strange, isn't it? The limitations of the human psyche." Where was he going with this? "You're brains are capable of so much more than you use them for, yet, you dwindle that away until you're left with nothing." He looked at John with a look that was distinctly not Rodney and John began to feel worried for his friend's sanity.

Rodney walked to the dark window side of the office and placed a hand against the cold surface, staring at it as if he could see through the murky black depths of glass.

Maybe he could, John never did really know everything about his friend.

"It makes me wonder, what's the point? If humans waste such gifts, why are they around?" McKay turned to him and gave a smile that made a shiver go up John's spine. "And then I realized, if they don't deserve what they have, why do they deserve to be alive?"

Now John was close to panicking, why was Rodney acting like this, what was he saying?

"What the hell are you talking about?" John asked. "You're human too, McKay."

Rodney laughed darkly and looked down as he started to roll a paperweight around in his hand.

"You really haven't figured it out, have you?" He asked, walking up to the desk, "Are you really that bad of a friend Sheppard, that you didn't notice what was happening to him before Col. Carter's." He let out a sharp laugh. " 'Accident'?"

"McKay…?" John was _really_ confused now, his friend was scaring him quite a bit. "What are you saying?"

"You really are oblivious col." Rodney turned the paperweight around several more times. "Do you really think that Col. Carter just _happened_ to be put into a coma by a random explosion. Or a naqauda generator overloaded yet only destroyed the room it was in?" Rodney let out a dark chuckle. "Or that Dr. Keller was beaten to death by nothing?"

"No." John gasped as the reality of what Rodney was saying sunk in. "Rodney… No, you didn't do that, you didn't kill them."

"No…" Suddenly John found himself pressed up against a wall by his throat, blood red eyes staring at him where Rodney's normally blue ones would be. "He didn't."

--

Yup, plots wrapping itself up, also, thinking of changing the title, but can't think of one.

Also have plans for the fan fic I work on after this, but not spilling the details.


	13. Chapter 13

Notes to reviewers of last chapter:

Angw: Hope is fleeting.

Miss pookamonga: Thanks, I'm glad you like the story.

Samandjackforever: Yes, we love cliffhangers. Especially with ketchup.

Rodnii: (Love your name BTW) I am so glad you like this story, and I'll try to make the chapters longer.

I don't own stargate, Atlantis or otherwise.

--

He had John pressed up to the wall by his throat, content in watching the life of the colonel slowly slip away between his fingers.

What he hadn't counted on was John being able to think a lot faster than he let on… And his desk being within legs reach of the wall.

Sheppard kicked his legs out and knocked the desk over, not only shattering several glass items, but also making enough noise to wake the dead.

He immediately caught on to what he was doing and growled before delivering a sharp blow to the temple, causing the colonel to slump in his grip before hitting the floor like a ragdoll when he let go.

He turned around to face the door sharply when there was a knocking.

"Sir?" Lorne's voice came through. "Is everything all right? Sir?"

He looked around quickly, already formulating a plan.

Reaching down and grabbing a particularly sharp piece of glass, he went and stood behind the door.

"Sir?"

He cleared his throat.

"What do you want?" He snapped in a perfect imitation of his host when angry.

"Dr. McKay I heard a crash, is everything all right?"

"I would probably tell you yes, everything's fine, but you, with your tiny military brain, would fail to grasp that and will come in no matter what I say, so come in and get it over with."

There was a pause before the door slowly pushed open, shortly followed by Lorne taking slow, cautious steps in.

He walked slowly to the center of the room, surveying the wreckage of what used to be a desk, before the door closed itself behind him.

He whipped around and saw Dr. McKay staring at the ground.

"Dr. McKay. You scared me there."

He saw the smaller man give a silent chuckle and felt liquid nitrogen run up his spine, he instinctively moved his hand to his gun.

The second he did that he felt himself be thrown down to the ground, glass crunching as his body pushed down on it.

Before he could register what was happening, Dr. McKay was leaning over him, only, it wasn't him, not quite. If it was him, he wouldn't have had that cruel smirk twisting across his face, nor would he have had demonic red eyes glowing in the dim light.

Before he could even think to fight back, Lorne saw a flash of something and felt searing pain rip through his neck before a warm substance bubbled up into his mouth. It was blood, he realized in panic. He was going to die.

He couldn't breathe, it was like he was drowning, oh god, his neck burnt so much.

And then the world went dark for Evan Lorne.

He stood up and looked down at the body of the dead major, feeling nothing but triumph at not only getting another pest out of the way, but getting another weapon to help him.

He took the gun off of the man's body before turning to the door.

--

And now we wait for the Lorne fans to kick my ass.


	14. Chapter 14

Notes to reviewers of last chapter:

Miss Pookamonga: I feel so bad for killing him, but I regret nothing. And some friends of mine have read the last chapter and this one and are encouraging me to change one of the genres to horror.

Gabumon: Yeah, I'll probably go back and re-write the chapter, I was suffering from a mild fever when I wrote that (I seem to get terrible fevers quite often around this point in time)

Angw: I feel so terrible for making him do that, ugh, bad Emma!

--

They never saw it coming.

It had all been an average day in the gateroom, nothing unexpected, nothing going wrong…

That should have been their first clue.

When Dr. McKay had first come in it hadn't caused too much surprise, the only surprise that they really felt was at him showing up after not coming anywhere near the gateroom for a few weeks, if they'd even bothered to pay that much attention they would have seen that something was wrong right away and they never would have let him get in to see colonel Sheppard.

But things didn't go that way, as it were, people were too wrapped up in themselves to open their eyes to what would have been obvious if they'd only looked close enough, if they'd only cared.

No one beyond Lorne had really seen much to worry about when the crash had come from the main office, everyone had decided that it probably was McKay and Sheppard getting into an argument about something or one of them accidentally knocked the desk over while they were talking.

No one really thought it to be anything close to what it was.

So Lorne had gone into the office, everyone thought that that was it, that it was the end of something not even worth mentioning in their daily logs.

But then half-an-hour passed and when Lorne didn't reemerge, and there were no other sounds coming from the office, that was when they started to worry.

It had started off as a speckle of doubt, someone wondering in passing why Lorne was taking so long, after that it had slowly gone downhill, imagine a sled going down a steep icy hill with an ice pick in the snow behind it, it will still reach the bottom, it'll just take a lot longer than it should in order to get there.

That was what the gatroom was like, it slowly coming to each of them just how wrong the situation that was going on was.

But it was already well along its way to becoming too late for them, too late for any of them, for at that moment they were being watched, by one of the very people they were trying to figure out what was wrong with.

He had at first played about with the idea of simply coming out the door and taking control of Atlantis that way, but had quickly dismissed that idea, even with his advanced being there was no way he'd be able to go up against them without some element of surprise.

So he'd snuck out through the balcony, knowing that he would lose his edge if he came out through the main door, and waited, letting them slowly become more paranoid with what was going on, waiting for just the right moment to strike.

He watched from the shadows, not moving, barely breathing, invisible to them, but he remained there, waiting for the perfect moment to strike.

Minutes passed, maybe even hours, before he saw his chance.

He stood with a grace his host would have never shown, moving silently up behind one of the gate technicians, their names were unimportant to him, and raising his smaller hand gun to her head while keeping a hand on the hilt of the larger weapon, ready for the full out attack when he brought forth the next part of his plan.

His eyes narrowed and a dark smirk spread across his face as his eyes glowed a bloody red, he waited three seconds to make sure that all was aligned properly before pulling down on the trigger.

It happened so quickly that no one had any time to register it, the bullet drove through her skull like it was made of jello, also slamming a good five inches into the control panel she was at as well. The noise seemed to make time freeze for two seconds before everyone turning to him.

They stared at him in silence and in shock for several seconds before he raised the other gun, smirking with a dangerous fire in his eyes.

They never saw it coming.

--

For those of you who've read my story "Lycanthrope" over on Fictionpress, you'll notice I used the same style of using the same sentence I started the chapter with to end it.


	15. Chapter 15

Notes to reviewers of last chapter:

Miss Pookamonga: Whenever I work on this story I'm torn between crying and laughing maniacally, is that weird?

Nexis44: Aye aye! Update is here!

I own nofing

--

The alarm going off had been a wake-up call no one on Atlantis really wanted, blaring through every hallway, every lab, and every room that had been explored.

After the first few moments of shock wore off the entire base sprung into a practiced procedure, they had no clue what was going on but they had no idea what to do besides the procedure, well, most of the scientists didn't, the others had some field experience to put to use, but they all followed the standard procedure because they saw no reason to do otherwise.

The scientists switched off from whatever program they were working on and started working to access the system to figure out what was wrong, the soldiers all made their way to the armory before going to the labs to find out what was going on, and anyone who wasn't able to do either got to a safe place or worked to find a way to help if they could.

It hadn't taken long for the scientists to get into the CCTV feed in the tower, and what they saw created a stir of emotions to run through the group assembled, mostly shock, occasional disbelief, and there was always the one out of five who felt their insides churn with nausea as they watched what was happening on the screen.

There had been twenty-five people working in the gateroom that day, when they turned the camera on only eleven were left, running and _screaming_ from their attacker, and it was their attacker that shocked everyone the most.

There, with guns going off, was their very own head scientist, Rodney McKay.

"McKay?" A soldier asked, more to himself than anyone, as he stared at the screen in disbelief. "Is that _really_-" A scientist cut him off, shaking her head.

"It can't be, must be some sort of trick."

"It can't be a trick, McKay just finally snapped." Another scientist threw in, eyes not leaving the screen.

"I know that _Dr._ McKay can be a bit high strung, but he would _never_ do this."

"What do you know about our _boss_ who we rarely say words to outside of work?"

"A hell of a lot more than yo-" The scientist was cut off by Dr. Mallozzi, who was running the screen.

"Look!" He shouted, silencing the room. "It doesn't matter whether or not it's a trick, we need to get in there and stop…" He paused, glancing at the screen. "Whoever that is, from doing whatever it is they're planning."

They all started murmuring amongst themselves, trying to figure out what to do and who would go when a loud, piercing static caught their attention.

"And we just lost live feed." Dr. Mallozzi said irritably to himself before addressing the room. "We need someone to go in there, to try and hold him off while we organize a larger effort, normally I'd recommend sending more in, but he's closed off the doors and we can only guarantee being able to hotwire them each open long enough for one person to get through before he realizes what we're doing and shuts them off completely."

A scientist spoke up, "That makes no sense! How would he be able to-"

"Because of this." Dr. Mallozzi rewound back and zoomed in to show that McKay, or at least the one who looked like McKay, was holding a mini-datapadd. "From what I can tell the eleven left are only scientists, they won't last much longer and they definitely won't stand a chance against him if he pauses for only a few seconds to issue the commands, he probably hasn't realized that the alarm has gone off yet, or if he has he isn't thinking much of it, so I repeat: We need someone to go up there."

There was a long silence, or at least what felt like a long silence as only about ten seconds passed, before Dr. Mallozzi spoke again, "Is there anyone willing to go up there?" There was a hint of desperation in his voice as he looked over the crowd gathered.

From the very back of the room, coming from the doorframe actually, a voice spoke up, "I'll go."

Everyone turned, some faster than others but none were really all that slow, and stared in open mouthed with their jaws scraping the floor shock when they saw the owner of the voice.

There, standing in the doorway, clad in a dark blue tee shirt and black pants, was Col. Samantha Carter.

--

Next chapter, final chapter. Start making funeral plans because I've had the ending typed up for months and just need to make a few edits.

Oh, BTW, Dr. Mallozzi was a throwaway gag in "Sunday" and I thought "Hey, what the hell? Let's throw him in there so I don't have to come up with some lame-ass name."


	16. End

Notes to reviewer of last chapter:

Miss Pookamonga: Updated! I hope you like this, because, you know, it's the end.

I ownz nofing

--

"Are you sure about this Col.?" A Sgt. asked her as they stood outside the first door.

Sam nodded, "Positive, it's my fault that he managed to get this far, I should be the only one to go in there alone." She took a handgun from another soldier, it was all she could take, a P90 or any other large gun would weigh her down.

"Okay Col. we're ready, go stand in front of the door," Dr. Mallozzi said, Sam moved away from the group and stood in front of the door. "Listen, Col." Dr. Mallozzi sighed. "Are you sure it should be you to do this? You just woke up out of a coma."

Sam nodded. "It should be me, no one else." Seeing that Dr. Mallozzi and several others, including Ronon and Teyla who were standing at the very edge of the crowd, were about to protest she barked out a quick, "That's an order." And they all went silent.

"Now." Dr. Mallozzi typed a few things into the computer. "You'll have three seconds to get through each door, after each you only have eleven seconds to get to the next one, there are five doors in between here and the gateroom not counting this first one." His hand hovered over the last key. "This was the closest entrance we could find."

Sam nodded, "Understood. Ready when you are."

Dr. Mallozzi nodded before starting the countdown. "Five… Four… Three… Two… Go!" The doors opened and Sam took off running, she was lucky, they were straight corridors in between each door, but she still had to run fast.

She made it to the second door five seconds before it opened, she took deep breaths as she waited for the door to open, the second it did she was off again.

She had to push herself harder the second time, her lungs had started burning and it was all she could do to ignore the way her legs were cramping up.

She reached that door with three seconds to spare.

This continued for the remaining doors until she had to _dive_ through the last one.

Sam rolled into the room, just barely making it before the doors closed behind her. Her eyes scanned the room as she took deep breaths in an attempt to remain calm, she slowly stood up.

And there it was. It was firing a shot into the head of the last scientist left alive in the room, a finger pressed to a button on his Mini-datapadd.

Then only she and it were left.

It turned and began typing several things into a consol. Smirking as it did so.

Sam gulped and pulled out her gun, she didn't want to use it and prayed that she wouldn't have to. But if worse came to worse…

It smirked, turning to face her.

"I would have thought that you'd be dead by now, the human body can't really survive the type of coma I put you in for very long."

Sam glared.

"For something that claims to be smarter than the host it took, you make the same mistake of underestimating me." She tried her best to sound tough, but it was hard when the thought of what she'd have to almost undoubtedly do forced her to choke back tears.

It knew that she is trying not to cry and simply grins in pleasure. Moving toward her.

"Oh, I think I underestimated your determination, not something I'll do again, but I _overestimated_ your emotional capacity for this." He stood right in front of her now, her hands shook and she nearly dropped the gun, just barely keeping it in her grip.

He smirked, placing a hand to her cheek, his touch burned her, yet at the same time it chilled her to the core.

"Go ahead, Sam." His voice was soft. "Kill me, end this."

She glanced into his eyes and saw no emotion. Just the endless void of red that had taken over what was once a brilliant blue.

She took the gun and pressed it to his heart. All she had to do was pull the trigger and he would no longer be a threat. He would be gone.

Taking Rodney with him.

A shiver ran down her spine and tears slowly dripped from her eyes.

Sam gulped and took a step back letting her arm drop and the gun fall, she couldn't do it…

He smirked and walked away.

"That's what I thought." He said, going back to the consol. He might have forgotten the gun or he might have decided that she was no longer any threat to him, whatever it was he left the gun on the floor and her standing there. His plan was more than likely to torment her with the silence of her not being able to stop him before killing her when they reached the end.

Sam slowly sank to her knees, not even paying attention to the gun that lay mere inches from her, forgotten by her and ignored by him.

How come she hadn't killed him when she had the chance? Is it because that no matter how much she knew of him being… The monster that he is, she would always think of him as Rodney?

And no matter how hard she tried she could never kill him?

Sam clenched her eyes shut.

_He is not Rodney… Not anymore. You know what you have to do. _She told herself, desperate to believe the words.

Suddenly, alarms started blaring.

"What's happening?" She called, her voice wavering as she picked up the gun.

"They've finally figured out how to get in." It chuckled darkly, not even turning to face Sam, who was slowly approaching him. "So be it, when they finally get in I'll just dispose of them as well." It dismissed.

Sam took a deep breath and cocked the gun. The sound finally drawing its attention to her.

It turned around and smirked, believing that Sam was going to break down again.

He walked over and placed both his hands on her shoulders.

"Sam…" His voice was once again soft. "Do you really want to do this?" He asked, looking into her eyes.

Sam gulped and tears fell down her face.

"No." She whispered, causing it to smirk, believing that she had broken, that it had won.

A gunshot rang through the lab.

Blood splashed over both of them.

Its eyes widened before it fell back, Sam barely catching the body and laying it down gently.

It looked at her, indescribable rage boiling in its eyes.

"You may kill me, but you have also killed him." It hissed out, causing Sam to bite her lip and look away.

He growled for a few seconds before screaming.

Sam clenched her eyes shut and covered her ears. She couldn't listen to this.

"Sam." Came a voice, choked slightly.

Her eyes snapped open and she looked down to find blue eyes staring back at her.

"Rodney." She whispered before wrapping her arms around him, immediately pulling back when he gasped in pain.

"I… Am so sorry." She whispered, cradling his head in her arms.

"It's" He coughed, a small amount of blood escaping his lips. "Okay, you did the right thing." He smiled, reaching up and touching her face.

This time his touch didn't burn her, nor did it freeze her. This time it was just there. And that was what she needed.

"I'm… Going to die, huh?" He asked, breaking the silence that Sam had been clinging to.

Sam swallowed the lump in her throat.

"No," she said, shaking her head. "That, t-that thing's gone, we can save you."

Rodney looked at her for a few seconds, his gaze starting out as hopeful but ending in sorrow and resignation.

"No." He coughed, more blood spurting from his lips. "I can't let you do that." He hissed in pain, causing a few more tears to run down Sam's face. "It's still there Sam, I can feel it, you can't save me…" He reached up a hand and cradled her face. "Not this time."

Sobs racked through Sam's body, the tears sliding off of her face and onto Rodney's, mingling with his own.

"I love you Sam…" He coughed, getting so much weaker very quickly. "I have ever since we first met. I don't want you to forget that."

"I…" She gulped, there it was, the three words she had never really said to him, to most anyone really, a million questions ran through her head at a million miles per hour, would she mean it? Would saying it just bring that much more pain to her after his death? Was it something she could say without feeling like her heart was breaking?

Deep down she knew that saying it would cause her heart to break, she only wished that she could have realized the truth behind what she was going to say under very different circumstances.

"I love you too." She whispered before bending down and placing her lips on his for a brief moment.

Their first kiss…

And their last.

When Sam pulled away she saw him smile at her one last time before his eyes closed and he stopped breathing.

Sam gave a small smile as she looked over him before it all caught up to her, she took in a shakey breath before sobbing and falling to the ground next to the body, reaching for the gun that she had dropped at some point during her talk with Rodney.

But something made her pause for a brief moment as she looked over Rodney.

_"You can't save me Sam… Not this time."_

_"I love you Sam."_

Sam bit her lip and drew in a shakey breath, the gun trembling in her hands, and looked at the door, which was sparking from them beginning to cut through to get over.

She gave a small sob and cradled Rodney's head, brushing some dried blood that had most likely splattered onto him earlier, before placing the gun to her temple.

"I'm sorry." She whispered. "I'm _so_ sorry."

--

*Sob* That's the end. I can't believe I could bring myself to write that. Bad Emma! Don't kill off McKay again!

And I made the ending like that on purpose, although I'm pretty sure that all of you probably have a good guess as to what happened…

Now that I've actually completed the story I feel depressed about it being gone.

Most of you are probably wondering why I skipped the reactions to Col. Carter being alive, well, originally I had this scene in mind where she explained to them what was going on, but I couldn't for the hell of me write it as more than a recap.

You also may be wondering why I didn't give Teyla and Ronon a bigger place in this chapter, well, originally it was going to start off with Teyla and Ronon talking to her, but I was never satisfied with how that came out so I had to scrap it.

If anyone's interested I've started an RP board, not for Stragate but I'm going to be putting up fan RPs at some point, link: http:// thestoryboards. 21. forumer. com Just remove the spaces. Seriously, join, I'm the only member.

And hate mail for the ending in 3… 2…


End file.
